United sealed their passage into the last 16 of the Europa League with a 1-0 win over St Etienne on Wednesday.
They face a hectic fixture list over the next few weeks and their game at Stamford Bridge will be played on March 13, sandwiched between their Europa League last-16 first and second legs.
Mourinho is angry that the date was announced before the Europa League draws are conducted this Friday.
“Of course and I feel really surprised that the decision is made before our draw in Europe,” he said.
“Because in this moment nobody knows where we play, nobody knows where the first and second matches are. Imagine we play Chelsea on Monday and then we have to go to the second match in Europe in Russia, Turkey or Greece.
“I think once more the interests, they go in front of the clubs and English football’s interests, and nobody cares about it. But this is what I have.
“I cannot play against Chelsea with the second team. I cannot play against Chelsea with the U21s like Manchester City did last year. I cannot do that – we are Manchester United.
“I don’t do that as Manchester United manager. I don’t do that to the FA Cup because the FA Cup is not guilty of these decisions. The FA Cup is beautiful, the competition is historical. I have to treat Manchester United supporters and the FA Cup in the right way.
“I cannot go there with U21s. Probably they would deserve it, but I don’t do that, so what is going to happen is an accumulation of matches.
“People playing a lot of matches, I have to make some rotation but some of the boys will have to play in all these consecutive matches”, he said.